Multiple sequence alignment - TraesCS1D01G027000

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1D01G027000 chr1D 100.000 3904 0 0 1 3904 10842827 10846730 0.000000e+00 7210.0
1 TraesCS1D01G027000 chr1D 91.271 2887 171 38 1001 3848 10764303 10761459 0.000000e+00 3860.0
2 TraesCS1D01G027000 chr1D 88.614 1537 132 24 1654 3156 10836442 10837969 0.000000e+00 1829.0
3 TraesCS1D01G027000 chr1D 87.515 825 68 12 3027 3824 10773847 10773031 0.000000e+00 920.0
4 TraesCS1D01G027000 chr1D 84.606 864 79 26 3027 3845 10931697 10932551 0.000000e+00 809.0
5 TraesCS1D01G027000 chr1D 86.585 82 9 2 2978 3058 10762318 10762238 5.370000e-14 89.8
6 TraesCS1D01G027000 chr1D 98.000 50 1 0 3844 3893 474108512 474108561 1.930000e-13 87.9
7 TraesCS1D01G027000 chr1D 91.935 62 2 3 3833 3893 46474781 46474840 2.500000e-12 84.2
8 TraesCS1D01G027000 chr1D 90.476 63 5 1 3829 3891 357699427 357699366 8.990000e-12 82.4
9 TraesCS1D01G027000 chr1A 91.937 2158 117 33 893 3029 22791346 22789225 0.000000e+00 2968.0
10 TraesCS1D01G027000 chr1A 89.761 2051 144 24 1654 3659 13255835 13257864 0.000000e+00 2564.0
11 TraesCS1D01G027000 chr1A 90.312 1920 144 25 1001 2910 13229021 13230908 0.000000e+00 2477.0
12 TraesCS1D01G027000 chr1A 91.009 1824 125 24 1098 2911 13009792 13007998 0.000000e+00 2423.0
13 TraesCS1D01G027000 chr1A 92.719 1552 91 14 1379 2922 13212771 13214308 0.000000e+00 2220.0
14 TraesCS1D01G027000 chr1A 92.548 671 26 7 3023 3678 22778886 22778225 0.000000e+00 941.0
15 TraesCS1D01G027000 chr1A 87.623 816 68 13 3027 3815 13214328 13215137 0.000000e+00 917.0
16 TraesCS1D01G027000 chr1A 87.285 755 56 15 3027 3750 13230940 13231685 0.000000e+00 826.0
17 TraesCS1D01G027000 chr1A 84.522 827 80 23 3059 3846 13273868 13274685 0.000000e+00 774.0
18 TraesCS1D01G027000 chr1A 83.778 863 85 24 3027 3845 22760262 22759411 0.000000e+00 767.0
19 TraesCS1D01G027000 chr1A 87.576 491 27 11 846 1302 13212246 13212736 4.440000e-149 538.0
20 TraesCS1D01G027000 chr1A 96.743 307 10 0 1 307 455081380 455081686 2.690000e-141 512.0
21 TraesCS1D01G027000 chr1A 96.417 307 11 0 1 307 455079310 455079616 1.250000e-139 507.0
22 TraesCS1D01G027000 chr1A 92.647 340 17 4 311 650 22799849 22799518 2.110000e-132 483.0
23 TraesCS1D01G027000 chr1A 96.271 295 6 3 560 851 13193558 13193850 2.730000e-131 479.0
24 TraesCS1D01G027000 chr1A 85.714 385 31 10 3487 3854 13007670 13007293 6.120000e-103 385.0
25 TraesCS1D01G027000 chr1A 86.905 252 30 1 1027 1278 22773270 22773022 2.970000e-71 279.0
26 TraesCS1D01G027000 chr1A 88.182 220 26 0 1085 1304 13006348 13006129 2.990000e-66 263.0
27 TraesCS1D01G027000 chr1B 90.745 2161 137 41 798 2928 16225859 16223732 0.000000e+00 2824.0
28 TraesCS1D01G027000 chr1B 89.991 2128 120 41 849 2922 23896048 23898136 0.000000e+00 2663.0
29 TraesCS1D01G027000 chr1B 89.897 2128 122 41 849 2922 23597272 23599360 0.000000e+00 2652.0
30 TraesCS1D01G027000 chr1B 91.773 1410 104 9 1521 2922 39732725 39734130 0.000000e+00 1951.0
31 TraesCS1D01G027000 chr1B 93.740 1262 66 10 2170 3425 39807487 39808741 0.000000e+00 1881.0
32 TraesCS1D01G027000 chr1B 91.934 1339 85 15 1654 2971 23775595 23776931 0.000000e+00 1853.0
33 TraesCS1D01G027000 chr1B 91.250 1280 98 10 1653 2922 39814790 39816065 0.000000e+00 1731.0
34 TraesCS1D01G027000 chr1B 85.663 830 68 20 3027 3827 16223718 16222911 0.000000e+00 826.0
35 TraesCS1D01G027000 chr1B 86.178 709 62 12 3038 3718 23599391 23600091 0.000000e+00 734.0
36 TraesCS1D01G027000 chr1B 85.896 709 63 12 3038 3718 23898167 23898866 0.000000e+00 721.0
37 TraesCS1D01G027000 chr1B 82.807 855 88 32 3027 3845 16402091 16402922 0.000000e+00 710.0
38 TraesCS1D01G027000 chr1B 91.356 509 33 5 308 813 39803317 39803817 0.000000e+00 686.0
39 TraesCS1D01G027000 chr1B 84.959 605 44 27 893 1484 39806065 39806635 1.570000e-158 569.0
40 TraesCS1D01G027000 chr1B 84.456 386 49 8 928 1311 39732070 39732446 1.710000e-98 370.0
41 TraesCS1D01G027000 chr1B 85.630 341 36 8 3487 3817 39808759 39809096 2.890000e-91 346.0
42 TraesCS1D01G027000 chr1B 94.268 157 5 1 1367 1523 39732457 39732609 1.810000e-58 237.0
43 TraesCS1D01G027000 chr2D 98.371 307 5 0 1 307 408966654 408966960 1.230000e-149 540.0
44 TraesCS1D01G027000 chr2D 98.371 307 4 1 1 307 408964603 408964908 4.440000e-149 538.0
45 TraesCS1D01G027000 chr6B 97.394 307 8 0 1 307 447995958 447995652 1.240000e-144 523.0
46 TraesCS1D01G027000 chr6B 96.753 308 10 0 1 308 447993888 447993581 7.480000e-142 514.0
47 TraesCS1D01G027000 chr6B 91.935 62 2 3 3837 3897 171226457 171226516 2.500000e-12 84.2
48 TraesCS1D01G027000 chrUn 96.743 307 10 0 1 307 355652487 355652181 2.690000e-141 512.0
49 TraesCS1D01G027000 chrUn 94.643 56 1 2 3843 3897 83568273 83568219 6.950000e-13 86.1
50 TraesCS1D01G027000 chr3D 96.743 307 10 0 1 307 242068598 242068904 2.690000e-141 512.0
51 TraesCS1D01G027000 chr3D 96.743 307 10 0 1 307 242425816 242426122 2.690000e-141 512.0
52 TraesCS1D01G027000 chr2B 93.103 58 3 1 3841 3897 11402916 11402973 2.500000e-12 84.2
53 TraesCS1D01G027000 chr7D 92.982 57 2 2 3841 3897 282229724 282229670 8.990000e-12 82.4
54 TraesCS1D01G027000 chr7A 91.667 60 3 2 3830 3888 492243070 492243128 8.990000e-12 82.4
55 TraesCS1D01G027000 chr4A 90.323 62 5 1 3832 3893 648889425 648889485 3.230000e-11 80.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G027000 chr1D 10842827 10846730 3903 False 7210.000000 7210 100.000000 1 3904 1 chr1D.!!$F2 3903
1 TraesCS1D01G027000 chr1D 10761459 10764303 2844 True 1974.900000 3860 88.928000 1001 3848 2 chr1D.!!$R3 2847
2 TraesCS1D01G027000 chr1D 10836442 10837969 1527 False 1829.000000 1829 88.614000 1654 3156 1 chr1D.!!$F1 1502
3 TraesCS1D01G027000 chr1D 10773031 10773847 816 True 920.000000 920 87.515000 3027 3824 1 chr1D.!!$R1 797
4 TraesCS1D01G027000 chr1D 10931697 10932551 854 False 809.000000 809 84.606000 3027 3845 1 chr1D.!!$F3 818
5 TraesCS1D01G027000 chr1A 22789225 22791346 2121 True 2968.000000 2968 91.937000 893 3029 1 chr1A.!!$R4 2136
6 TraesCS1D01G027000 chr1A 13255835 13257864 2029 False 2564.000000 2564 89.761000 1654 3659 1 chr1A.!!$F2 2005
7 TraesCS1D01G027000 chr1A 13229021 13231685 2664 False 1651.500000 2477 88.798500 1001 3750 2 chr1A.!!$F5 2749
8 TraesCS1D01G027000 chr1A 13212246 13215137 2891 False 1225.000000 2220 89.306000 846 3815 3 chr1A.!!$F4 2969
9 TraesCS1D01G027000 chr1A 13006129 13009792 3663 True 1023.666667 2423 88.301667 1085 3854 3 chr1A.!!$R6 2769
10 TraesCS1D01G027000 chr1A 22778225 22778886 661 True 941.000000 941 92.548000 3023 3678 1 chr1A.!!$R3 655
11 TraesCS1D01G027000 chr1A 13273868 13274685 817 False 774.000000 774 84.522000 3059 3846 1 chr1A.!!$F3 787
12 TraesCS1D01G027000 chr1A 22759411 22760262 851 True 767.000000 767 83.778000 3027 3845 1 chr1A.!!$R1 818
13 TraesCS1D01G027000 chr1A 455079310 455081686 2376 False 509.500000 512 96.580000 1 307 2 chr1A.!!$F6 306
14 TraesCS1D01G027000 chr1B 23775595 23776931 1336 False 1853.000000 1853 91.934000 1654 2971 1 chr1B.!!$F2 1317
15 TraesCS1D01G027000 chr1B 16222911 16225859 2948 True 1825.000000 2824 88.204000 798 3827 2 chr1B.!!$R1 3029
16 TraesCS1D01G027000 chr1B 39814790 39816065 1275 False 1731.000000 1731 91.250000 1653 2922 1 chr1B.!!$F3 1269
17 TraesCS1D01G027000 chr1B 23597272 23600091 2819 False 1693.000000 2652 88.037500 849 3718 2 chr1B.!!$F4 2869
18 TraesCS1D01G027000 chr1B 23896048 23898866 2818 False 1692.000000 2663 87.943500 849 3718 2 chr1B.!!$F5 2869
19 TraesCS1D01G027000 chr1B 39803317 39809096 5779 False 870.500000 1881 88.921250 308 3817 4 chr1B.!!$F7 3509
20 TraesCS1D01G027000 chr1B 39732070 39734130 2060 False 852.666667 1951 90.165667 928 2922 3 chr1B.!!$F6 1994
21 TraesCS1D01G027000 chr1B 16402091 16402922 831 False 710.000000 710 82.807000 3027 3845 1 chr1B.!!$F1 818
22 TraesCS1D01G027000 chr2D 408964603 408966960 2357 False 539.000000 540 98.371000 1 307 2 chr2D.!!$F1 306
23 TraesCS1D01G027000 chr6B 447993581 447995958 2377 True 518.500000 523 97.073500 1 308 2 chr6B.!!$R1 307

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
413 414 0.106519 ATTCAAATGGAGGAGCCCGG 60.107 55.0 0.0 0.0 34.97 5.73 F
1041 3297 0.264359 AGGATGAGGAGGAGGAGGTG 59.736 60.0 0.0 0.0 0.00 4.00 F
1042 3298 0.762461 GGATGAGGAGGAGGAGGTGG 60.762 65.0 0.0 0.0 0.00 4.61 F
1788 4219 2.107950 TGGTTTAACTCAGCGGGATG 57.892 50.0 0.0 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1360 3634 2.889045 TCAGCTCCCATACATACCGTAC 59.111 50.000 0.0 0.0 31.27 3.67 R
1950 4399 3.238597 GGAAGCCTACATCTGAGGAGAT 58.761 50.000 0.0 0.0 39.75 2.75 R
2006 4829 7.770433 AGATAAATGCACTTGTAGTCAATGCTA 59.230 33.333 0.0 0.0 37.20 3.49 R
3312 7416 3.079578 ACAGAAGTGACCATGAGCAATG 58.920 45.455 0.0 0.0 35.89 2.82 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 130 2.352503 GCACCACGCAATTGATCTTT 57.647 45.000 10.34 0.00 41.79 2.52
130 131 1.987770 GCACCACGCAATTGATCTTTG 59.012 47.619 10.34 1.12 41.79 2.77
131 132 2.598589 CACCACGCAATTGATCTTTGG 58.401 47.619 10.34 9.32 0.00 3.28
132 133 1.067635 ACCACGCAATTGATCTTTGGC 60.068 47.619 10.34 0.00 0.00 4.52
133 134 1.632422 CACGCAATTGATCTTTGGCC 58.368 50.000 10.34 0.00 0.00 5.36
134 135 1.203052 CACGCAATTGATCTTTGGCCT 59.797 47.619 10.34 0.00 0.00 5.19
135 136 1.203052 ACGCAATTGATCTTTGGCCTG 59.797 47.619 10.34 0.00 0.00 4.85
136 137 1.203052 CGCAATTGATCTTTGGCCTGT 59.797 47.619 10.34 0.00 0.00 4.00
137 138 2.353011 CGCAATTGATCTTTGGCCTGTT 60.353 45.455 10.34 0.00 0.00 3.16
138 139 3.119531 CGCAATTGATCTTTGGCCTGTTA 60.120 43.478 10.34 0.00 0.00 2.41
139 140 4.617995 CGCAATTGATCTTTGGCCTGTTAA 60.618 41.667 10.34 0.00 0.00 2.01
140 141 5.422145 GCAATTGATCTTTGGCCTGTTAAT 58.578 37.500 10.34 0.00 0.00 1.40
141 142 5.876460 GCAATTGATCTTTGGCCTGTTAATT 59.124 36.000 10.34 0.00 0.00 1.40
142 143 7.041107 GCAATTGATCTTTGGCCTGTTAATTA 58.959 34.615 10.34 0.00 0.00 1.40
143 144 7.010460 GCAATTGATCTTTGGCCTGTTAATTAC 59.990 37.037 10.34 0.00 0.00 1.89
144 145 7.716799 ATTGATCTTTGGCCTGTTAATTACA 57.283 32.000 3.32 0.00 34.95 2.41
164 165 8.877864 ATTACAGAATTTATTCTTGGTCCACA 57.122 30.769 2.27 0.00 44.28 4.17
165 166 6.575162 ACAGAATTTATTCTTGGTCCACAC 57.425 37.500 2.27 0.00 44.28 3.82
166 167 6.068010 ACAGAATTTATTCTTGGTCCACACA 58.932 36.000 2.27 0.00 44.28 3.72
167 168 6.549364 ACAGAATTTATTCTTGGTCCACACAA 59.451 34.615 2.27 0.00 44.28 3.33
168 169 6.863126 CAGAATTTATTCTTGGTCCACACAAC 59.137 38.462 2.27 0.00 44.28 3.32
169 170 6.777580 AGAATTTATTCTTGGTCCACACAACT 59.222 34.615 0.00 0.00 44.28 3.16
170 171 5.766150 TTTATTCTTGGTCCACACAACTG 57.234 39.130 0.00 0.00 0.00 3.16
171 172 3.576078 ATTCTTGGTCCACACAACTGA 57.424 42.857 0.00 0.00 0.00 3.41
172 173 2.325583 TCTTGGTCCACACAACTGAC 57.674 50.000 0.00 0.00 0.00 3.51
173 174 0.937304 CTTGGTCCACACAACTGACG 59.063 55.000 0.00 0.00 0.00 4.35
174 175 1.092921 TTGGTCCACACAACTGACGC 61.093 55.000 0.00 0.00 0.00 5.19
175 176 1.522806 GGTCCACACAACTGACGCA 60.523 57.895 0.00 0.00 0.00 5.24
176 177 1.641677 GTCCACACAACTGACGCAC 59.358 57.895 0.00 0.00 0.00 5.34
177 178 1.087202 GTCCACACAACTGACGCACA 61.087 55.000 0.00 0.00 0.00 4.57
178 179 1.087202 TCCACACAACTGACGCACAC 61.087 55.000 0.00 0.00 0.00 3.82
180 181 1.153726 ACACAACTGACGCACACGA 60.154 52.632 0.00 0.00 43.93 4.35
181 182 0.529773 ACACAACTGACGCACACGAT 60.530 50.000 0.00 0.00 43.93 3.73
182 183 0.161658 CACAACTGACGCACACGATC 59.838 55.000 0.00 0.00 43.93 3.69
183 184 0.249280 ACAACTGACGCACACGATCA 60.249 50.000 0.00 0.00 43.93 2.92
184 185 1.070821 CAACTGACGCACACGATCAT 58.929 50.000 0.00 0.00 43.93 2.45
185 186 1.059692 CAACTGACGCACACGATCATC 59.940 52.381 0.00 0.00 43.93 2.92
186 187 0.528017 ACTGACGCACACGATCATCT 59.472 50.000 0.00 0.00 43.93 2.90
187 188 1.067565 ACTGACGCACACGATCATCTT 60.068 47.619 0.00 0.00 43.93 2.40
188 189 1.995484 CTGACGCACACGATCATCTTT 59.005 47.619 0.00 0.00 43.93 2.52
189 190 2.412870 TGACGCACACGATCATCTTTT 58.587 42.857 0.00 0.00 43.93 2.27
190 191 2.411748 TGACGCACACGATCATCTTTTC 59.588 45.455 0.00 0.00 43.93 2.29
191 192 1.732259 ACGCACACGATCATCTTTTCC 59.268 47.619 0.00 0.00 43.93 3.13
192 193 2.002586 CGCACACGATCATCTTTTCCT 58.997 47.619 0.00 0.00 43.93 3.36
193 194 2.029728 CGCACACGATCATCTTTTCCTC 59.970 50.000 0.00 0.00 43.93 3.71
194 195 2.029728 GCACACGATCATCTTTTCCTCG 59.970 50.000 0.00 0.00 35.56 4.63
195 196 3.511699 CACACGATCATCTTTTCCTCGA 58.488 45.455 0.00 0.00 33.74 4.04
196 197 4.115516 CACACGATCATCTTTTCCTCGAT 58.884 43.478 0.00 0.00 33.74 3.59
197 198 4.026228 CACACGATCATCTTTTCCTCGATG 60.026 45.833 0.00 0.00 38.64 3.84
198 199 4.142160 ACACGATCATCTTTTCCTCGATGA 60.142 41.667 4.65 4.65 46.94 2.92
199 200 4.805719 CACGATCATCTTTTCCTCGATGAA 59.194 41.667 6.11 0.00 46.27 2.57
200 201 5.291858 CACGATCATCTTTTCCTCGATGAAA 59.708 40.000 11.27 11.27 46.27 2.69
201 202 6.018425 CACGATCATCTTTTCCTCGATGAAAT 60.018 38.462 15.29 1.28 46.27 2.17
202 203 7.169813 CACGATCATCTTTTCCTCGATGAAATA 59.830 37.037 15.29 8.45 46.27 1.40
203 204 7.875041 ACGATCATCTTTTCCTCGATGAAATAT 59.125 33.333 15.29 10.07 46.27 1.28
204 205 8.167345 CGATCATCTTTTCCTCGATGAAATATG 58.833 37.037 20.74 20.74 46.27 1.78
205 206 7.734924 TCATCTTTTCCTCGATGAAATATGG 57.265 36.000 23.40 13.82 42.04 2.74
206 207 6.205464 TCATCTTTTCCTCGATGAAATATGGC 59.795 38.462 23.40 0.00 42.04 4.40
207 208 5.684704 TCTTTTCCTCGATGAAATATGGCT 58.315 37.500 15.29 0.00 34.41 4.75
208 209 5.528690 TCTTTTCCTCGATGAAATATGGCTG 59.471 40.000 15.29 3.10 34.41 4.85
209 210 2.771089 TCCTCGATGAAATATGGCTGC 58.229 47.619 0.00 0.00 0.00 5.25
210 211 2.104622 TCCTCGATGAAATATGGCTGCA 59.895 45.455 0.50 0.00 0.00 4.41
211 212 3.079578 CCTCGATGAAATATGGCTGCAT 58.920 45.455 0.50 0.00 0.00 3.96
212 213 3.119955 CCTCGATGAAATATGGCTGCATG 60.120 47.826 0.50 0.00 0.00 4.06
213 214 2.227149 TCGATGAAATATGGCTGCATGC 59.773 45.455 11.82 11.82 41.94 4.06
214 215 2.030628 CGATGAAATATGGCTGCATGCA 60.031 45.455 21.29 21.29 45.15 3.96
215 216 2.875087 TGAAATATGGCTGCATGCAC 57.125 45.000 18.46 13.69 45.15 4.57
216 217 1.065851 TGAAATATGGCTGCATGCACG 59.934 47.619 18.46 14.14 45.15 5.34
217 218 1.066002 GAAATATGGCTGCATGCACGT 59.934 47.619 18.46 12.26 45.15 4.49
218 219 0.664761 AATATGGCTGCATGCACGTC 59.335 50.000 18.46 15.02 45.15 4.34
219 220 0.464193 ATATGGCTGCATGCACGTCA 60.464 50.000 18.46 20.17 45.15 4.35
220 221 0.464193 TATGGCTGCATGCACGTCAT 60.464 50.000 27.99 27.99 45.15 3.06
221 222 1.317431 ATGGCTGCATGCACGTCATT 61.317 50.000 23.06 12.71 45.15 2.57
222 223 0.676151 TGGCTGCATGCACGTCATTA 60.676 50.000 18.46 0.00 45.15 1.90
223 224 0.664761 GGCTGCATGCACGTCATTAT 59.335 50.000 18.46 0.00 45.15 1.28
224 225 1.066002 GGCTGCATGCACGTCATTATT 59.934 47.619 18.46 0.00 45.15 1.40
225 226 2.480073 GGCTGCATGCACGTCATTATTT 60.480 45.455 18.46 0.00 45.15 1.40
226 227 3.181397 GCTGCATGCACGTCATTATTTT 58.819 40.909 18.46 0.00 42.31 1.82
227 228 3.241322 GCTGCATGCACGTCATTATTTTC 59.759 43.478 18.46 0.00 42.31 2.29
228 229 4.665212 CTGCATGCACGTCATTATTTTCT 58.335 39.130 18.46 0.00 31.79 2.52
229 230 4.413969 TGCATGCACGTCATTATTTTCTG 58.586 39.130 18.46 0.00 31.79 3.02
230 231 3.241322 GCATGCACGTCATTATTTTCTGC 59.759 43.478 14.21 0.00 31.79 4.26
231 232 4.413969 CATGCACGTCATTATTTTCTGCA 58.586 39.130 0.00 0.00 37.55 4.41
232 233 4.495911 TGCACGTCATTATTTTCTGCAA 57.504 36.364 0.00 0.00 30.48 4.08
233 234 4.225984 TGCACGTCATTATTTTCTGCAAC 58.774 39.130 0.00 0.00 30.48 4.17
234 235 4.023279 TGCACGTCATTATTTTCTGCAACT 60.023 37.500 0.00 0.00 30.48 3.16
235 236 4.917415 GCACGTCATTATTTTCTGCAACTT 59.083 37.500 0.00 0.00 0.00 2.66
236 237 5.402270 GCACGTCATTATTTTCTGCAACTTT 59.598 36.000 0.00 0.00 0.00 2.66
237 238 6.074356 GCACGTCATTATTTTCTGCAACTTTT 60.074 34.615 0.00 0.00 0.00 2.27
238 239 7.493313 CACGTCATTATTTTCTGCAACTTTTC 58.507 34.615 0.00 0.00 0.00 2.29
239 240 6.640907 ACGTCATTATTTTCTGCAACTTTTCC 59.359 34.615 0.00 0.00 0.00 3.13
240 241 6.640499 CGTCATTATTTTCTGCAACTTTTCCA 59.360 34.615 0.00 0.00 0.00 3.53
241 242 7.329226 CGTCATTATTTTCTGCAACTTTTCCAT 59.671 33.333 0.00 0.00 0.00 3.41
242 243 8.437742 GTCATTATTTTCTGCAACTTTTCCATG 58.562 33.333 0.00 0.00 0.00 3.66
243 244 6.783892 TTATTTTCTGCAACTTTTCCATGC 57.216 33.333 0.00 0.00 40.45 4.06
244 245 2.818130 TTCTGCAACTTTTCCATGCC 57.182 45.000 0.00 0.00 39.31 4.40
245 246 1.999648 TCTGCAACTTTTCCATGCCT 58.000 45.000 0.00 0.00 39.31 4.75
246 247 2.318908 TCTGCAACTTTTCCATGCCTT 58.681 42.857 0.00 0.00 39.31 4.35
247 248 3.495331 TCTGCAACTTTTCCATGCCTTA 58.505 40.909 0.00 0.00 39.31 2.69
248 249 3.894427 TCTGCAACTTTTCCATGCCTTAA 59.106 39.130 0.00 0.00 39.31 1.85
249 250 4.527816 TCTGCAACTTTTCCATGCCTTAAT 59.472 37.500 0.00 0.00 39.31 1.40
250 251 5.011943 TCTGCAACTTTTCCATGCCTTAATT 59.988 36.000 0.00 0.00 39.31 1.40
251 252 5.237048 TGCAACTTTTCCATGCCTTAATTC 58.763 37.500 0.00 0.00 39.31 2.17
252 253 5.011943 TGCAACTTTTCCATGCCTTAATTCT 59.988 36.000 0.00 0.00 39.31 2.40
253 254 5.934043 GCAACTTTTCCATGCCTTAATTCTT 59.066 36.000 0.00 0.00 34.03 2.52
254 255 6.427853 GCAACTTTTCCATGCCTTAATTCTTT 59.572 34.615 0.00 0.00 34.03 2.52
255 256 7.602265 GCAACTTTTCCATGCCTTAATTCTTTA 59.398 33.333 0.00 0.00 34.03 1.85
256 257 9.487790 CAACTTTTCCATGCCTTAATTCTTTAA 57.512 29.630 0.00 0.00 0.00 1.52
257 258 9.489084 AACTTTTCCATGCCTTAATTCTTTAAC 57.511 29.630 0.00 0.00 0.00 2.01
258 259 8.870116 ACTTTTCCATGCCTTAATTCTTTAACT 58.130 29.630 0.00 0.00 0.00 2.24
262 263 9.920946 TTCCATGCCTTAATTCTTTAACTATCT 57.079 29.630 0.00 0.00 0.00 1.98
263 264 9.561069 TCCATGCCTTAATTCTTTAACTATCTC 57.439 33.333 0.00 0.00 0.00 2.75
264 265 9.342308 CCATGCCTTAATTCTTTAACTATCTCA 57.658 33.333 0.00 0.00 0.00 3.27
281 282 9.979578 AACTATCTCAGATTGAGTAACATCATC 57.020 33.333 2.83 0.00 44.58 2.92
282 283 9.140874 ACTATCTCAGATTGAGTAACATCATCA 57.859 33.333 2.83 0.00 44.58 3.07
283 284 9.978044 CTATCTCAGATTGAGTAACATCATCAA 57.022 33.333 0.00 0.00 44.58 2.57
285 286 9.848710 ATCTCAGATTGAGTAACATCATCAATT 57.151 29.630 6.03 0.00 44.58 2.32
286 287 9.106070 TCTCAGATTGAGTAACATCATCAATTG 57.894 33.333 0.00 0.00 44.58 2.32
287 288 9.106070 CTCAGATTGAGTAACATCATCAATTGA 57.894 33.333 11.26 11.26 42.25 2.57
288 289 9.623000 TCAGATTGAGTAACATCATCAATTGAT 57.377 29.630 15.36 15.36 46.27 2.57
299 300 4.182693 CATCAATTGATGTTGTGGTGCT 57.817 40.909 31.74 2.41 45.10 4.40
300 301 3.921119 TCAATTGATGTTGTGGTGCTC 57.079 42.857 3.38 0.00 0.00 4.26
301 302 3.220940 TCAATTGATGTTGTGGTGCTCA 58.779 40.909 3.38 0.00 0.00 4.26
302 303 3.827876 TCAATTGATGTTGTGGTGCTCAT 59.172 39.130 3.38 0.00 0.00 2.90
303 304 5.008980 TCAATTGATGTTGTGGTGCTCATA 58.991 37.500 3.38 0.00 0.00 2.15
304 305 5.653330 TCAATTGATGTTGTGGTGCTCATAT 59.347 36.000 3.38 0.00 0.00 1.78
305 306 5.762825 ATTGATGTTGTGGTGCTCATATC 57.237 39.130 0.00 0.00 0.00 1.63
306 307 4.219264 TGATGTTGTGGTGCTCATATCA 57.781 40.909 0.00 0.00 0.00 2.15
310 311 4.587891 TGTTGTGGTGCTCATATCAATCA 58.412 39.130 0.00 0.00 0.00 2.57
324 325 3.870538 TCAATCAGGCCTATTGAGCAT 57.129 42.857 23.01 3.17 38.19 3.79
413 414 0.106519 ATTCAAATGGAGGAGCCCGG 60.107 55.000 0.00 0.00 34.97 5.73
431 432 2.593436 ACAGGGGCGAACGTTTGG 60.593 61.111 17.16 6.79 0.00 3.28
482 483 3.283751 TCCGTGTCCACAAAAGTTTGAT 58.716 40.909 10.66 0.00 40.55 2.57
567 568 3.270877 GCGTCCATCCAAATAGTTGTCT 58.729 45.455 1.80 0.00 32.40 3.41
568 569 4.439057 GCGTCCATCCAAATAGTTGTCTA 58.561 43.478 1.80 0.00 32.40 2.59
574 575 7.390718 GTCCATCCAAATAGTTGTCTAAAGTGT 59.609 37.037 1.80 0.00 32.40 3.55
576 577 8.883731 CCATCCAAATAGTTGTCTAAAGTGTAG 58.116 37.037 1.80 0.00 32.40 2.74
577 578 9.436957 CATCCAAATAGTTGTCTAAAGTGTAGT 57.563 33.333 1.80 0.00 32.40 2.73
578 579 9.654663 ATCCAAATAGTTGTCTAAAGTGTAGTC 57.345 33.333 1.80 0.00 32.40 2.59
579 580 8.644216 TCCAAATAGTTGTCTAAAGTGTAGTCA 58.356 33.333 1.80 0.00 32.40 3.41
582 583 9.826574 AAATAGTTGTCTAAAGTGTAGTCAACA 57.173 29.630 23.76 14.46 42.10 3.33
583 584 9.998106 AATAGTTGTCTAAAGTGTAGTCAACAT 57.002 29.630 23.76 15.55 42.10 2.71
584 585 9.998106 ATAGTTGTCTAAAGTGTAGTCAACATT 57.002 29.630 23.76 12.91 42.10 2.71
585 586 8.732746 AGTTGTCTAAAGTGTAGTCAACATTT 57.267 30.769 23.76 8.32 42.10 2.32
586 587 9.174166 AGTTGTCTAAAGTGTAGTCAACATTTT 57.826 29.630 23.76 8.05 46.29 1.82
587 588 9.783256 GTTGTCTAAAGTGTAGTCAACATTTTT 57.217 29.630 19.54 1.47 43.27 1.94
614 615 2.356278 TGGGCACTCCAAGGCATC 59.644 61.111 0.00 0.00 43.84 3.91
645 646 3.829601 CAGCCCCGTAGAGATAGATCTTT 59.170 47.826 0.00 0.00 37.25 2.52
651 652 7.546316 GCCCCGTAGAGATAGATCTTTAAAATC 59.454 40.741 0.00 0.00 37.25 2.17
744 748 8.959676 ATTTTACCAACTAAATCACCCCTAAA 57.040 30.769 0.00 0.00 0.00 1.85
952 3203 2.223735 CGCTCTAGGGTTTGCTCGATTA 60.224 50.000 0.00 0.00 0.00 1.75
1040 3296 0.560688 GAGGATGAGGAGGAGGAGGT 59.439 60.000 0.00 0.00 0.00 3.85
1041 3297 0.264359 AGGATGAGGAGGAGGAGGTG 59.736 60.000 0.00 0.00 0.00 4.00
1042 3298 0.762461 GGATGAGGAGGAGGAGGTGG 60.762 65.000 0.00 0.00 0.00 4.61
1289 3555 4.438880 CGACATCGATGAGGAGTGTAAGTT 60.439 45.833 31.33 4.13 43.02 2.66
1311 3577 5.224821 TGCCTCTATCTTCATCCTCAATG 57.775 43.478 0.00 0.00 36.65 2.82
1328 3596 5.304686 TCAATGAAGGTGGAGTACTGTTT 57.695 39.130 0.00 0.00 0.00 2.83
1330 3598 6.126409 TCAATGAAGGTGGAGTACTGTTTTT 58.874 36.000 0.00 0.00 0.00 1.94
1360 3634 6.093909 TGGCTGTTATGTGTACATTTCTGATG 59.906 38.462 0.00 0.00 37.76 3.07
1361 3635 6.094048 GGCTGTTATGTGTACATTTCTGATGT 59.906 38.462 0.00 0.00 37.76 3.06
1505 3809 5.639506 ACAGTGAATCTCAATCCGTTTACTG 59.360 40.000 0.00 0.00 41.30 2.74
1543 3965 5.408299 TGTATCAATTGACAACAGGAACTCG 59.592 40.000 11.07 0.00 34.60 4.18
1558 3980 3.426292 GGAACTCGCTGATTTGGCTAAAC 60.426 47.826 0.00 0.00 0.00 2.01
1614 4036 9.832445 TGATAGTTTTCTCTTGAAGTTAACAGT 57.168 29.630 8.61 0.00 33.28 3.55
1682 4108 6.803807 GCTTAACAACAGGAATCACTGATTTC 59.196 38.462 5.73 3.88 40.97 2.17
1782 4213 8.366671 ACGAATATTAGATGGTTTAACTCAGC 57.633 34.615 2.28 0.00 0.00 4.26
1788 4219 2.107950 TGGTTTAACTCAGCGGGATG 57.892 50.000 0.00 0.00 0.00 3.51
1893 4342 5.126396 TCCAATGCGATACTCTGATAGTG 57.874 43.478 0.00 0.00 39.39 2.74
1950 4399 5.116180 CAAACATCCTCTCCGTTAGCATAA 58.884 41.667 0.00 0.00 0.00 1.90
2006 4829 1.522355 CCGCGTCATTGCCAGAGAT 60.522 57.895 4.92 0.00 0.00 2.75
2813 6677 4.378046 CGAACCTTTGATTTAAGTCCACGG 60.378 45.833 0.00 0.00 0.00 4.94
3000 7065 3.383505 TGGACTGAGTTATATCGTGGTGG 59.616 47.826 0.00 0.00 0.00 4.61
3246 7346 7.479980 TGGCATTTTGTTAGACATGTATTAGC 58.520 34.615 0.00 0.00 0.00 3.09
3312 7416 9.059260 ACCATATTTATACCGTGGTTTGTATTC 57.941 33.333 0.00 0.00 40.08 1.75
3506 7645 0.685660 GTCCTTCCCGAGAAAGTGGT 59.314 55.000 0.00 0.00 0.00 4.16
3548 7689 4.141846 TGCCTGTTCAAGCCAATACAAAAA 60.142 37.500 0.00 0.00 0.00 1.94
3551 7692 6.048509 CCTGTTCAAGCCAATACAAAAACTT 58.951 36.000 0.00 0.00 0.00 2.66
3709 7869 8.581578 TGTGGATATGCTAATTTACGACATCTA 58.418 33.333 0.00 0.00 0.00 1.98
3746 7906 9.809395 TCTGCTACATCAAGTATATTACCTAGT 57.191 33.333 0.00 0.00 30.93 2.57
3827 7990 4.782019 TGTGAATGTCATTAGCCCAAAC 57.218 40.909 0.00 0.00 0.00 2.93
3829 7992 4.586421 TGTGAATGTCATTAGCCCAAACAA 59.414 37.500 0.00 0.00 0.00 2.83
3830 7993 5.069648 TGTGAATGTCATTAGCCCAAACAAA 59.930 36.000 0.00 0.00 0.00 2.83
3831 7994 5.405269 GTGAATGTCATTAGCCCAAACAAAC 59.595 40.000 0.00 0.00 0.00 2.93
3832 7995 5.069648 TGAATGTCATTAGCCCAAACAAACA 59.930 36.000 0.00 0.00 0.00 2.83
3833 7996 5.543507 ATGTCATTAGCCCAAACAAACAA 57.456 34.783 0.00 0.00 0.00 2.83
3834 7997 4.688021 TGTCATTAGCCCAAACAAACAAC 58.312 39.130 0.00 0.00 0.00 3.32
3835 7998 4.404073 TGTCATTAGCCCAAACAAACAACT 59.596 37.500 0.00 0.00 0.00 3.16
3836 7999 4.982295 GTCATTAGCCCAAACAAACAACTC 59.018 41.667 0.00 0.00 0.00 3.01
3837 8000 4.646945 TCATTAGCCCAAACAAACAACTCA 59.353 37.500 0.00 0.00 0.00 3.41
3838 8001 5.304101 TCATTAGCCCAAACAAACAACTCAT 59.696 36.000 0.00 0.00 0.00 2.90
3839 8002 3.457610 AGCCCAAACAAACAACTCATG 57.542 42.857 0.00 0.00 0.00 3.07
3840 8003 3.030291 AGCCCAAACAAACAACTCATGA 58.970 40.909 0.00 0.00 0.00 3.07
3841 8004 3.642848 AGCCCAAACAAACAACTCATGAT 59.357 39.130 0.00 0.00 0.00 2.45
3842 8005 4.101430 AGCCCAAACAAACAACTCATGATT 59.899 37.500 0.00 0.00 0.00 2.57
3843 8006 4.815846 GCCCAAACAAACAACTCATGATTT 59.184 37.500 0.00 0.00 0.00 2.17
3844 8007 5.296531 GCCCAAACAAACAACTCATGATTTT 59.703 36.000 0.00 0.00 0.00 1.82
3845 8008 6.481644 GCCCAAACAAACAACTCATGATTTTA 59.518 34.615 0.00 0.00 0.00 1.52
3846 8009 7.011857 GCCCAAACAAACAACTCATGATTTTAA 59.988 33.333 0.00 0.00 0.00 1.52
3847 8010 8.334632 CCCAAACAAACAACTCATGATTTTAAC 58.665 33.333 0.00 0.00 0.00 2.01
3848 8011 8.334632 CCAAACAAACAACTCATGATTTTAACC 58.665 33.333 0.00 0.00 0.00 2.85
3849 8012 7.692908 AACAAACAACTCATGATTTTAACCG 57.307 32.000 0.00 0.00 0.00 4.44
3850 8013 7.033530 ACAAACAACTCATGATTTTAACCGA 57.966 32.000 0.00 0.00 0.00 4.69
3851 8014 7.484975 ACAAACAACTCATGATTTTAACCGAA 58.515 30.769 0.00 0.00 0.00 4.30
3852 8015 7.976734 ACAAACAACTCATGATTTTAACCGAAA 59.023 29.630 0.00 0.00 0.00 3.46
3853 8016 8.812329 CAAACAACTCATGATTTTAACCGAAAA 58.188 29.630 0.00 0.00 41.24 2.29
3854 8017 8.934507 AACAACTCATGATTTTAACCGAAAAA 57.065 26.923 0.00 0.00 40.39 1.94
3855 8018 8.574196 ACAACTCATGATTTTAACCGAAAAAG 57.426 30.769 0.00 0.00 40.39 2.27
3856 8019 7.651704 ACAACTCATGATTTTAACCGAAAAAGG 59.348 33.333 0.00 0.00 40.39 3.11
3857 8020 6.156519 ACTCATGATTTTAACCGAAAAAGGC 58.843 36.000 0.00 0.00 40.39 4.35
3858 8021 6.015434 ACTCATGATTTTAACCGAAAAAGGCT 60.015 34.615 0.00 0.00 40.39 4.58
3859 8022 6.754193 TCATGATTTTAACCGAAAAAGGCTT 58.246 32.000 0.00 0.00 40.39 4.35
3860 8023 7.213678 TCATGATTTTAACCGAAAAAGGCTTT 58.786 30.769 6.68 6.68 40.39 3.51
3861 8024 7.383843 TCATGATTTTAACCGAAAAAGGCTTTC 59.616 33.333 13.76 0.41 40.39 2.62
3863 8026 2.691984 TAACCGAAAAAGGCTTTCGC 57.308 45.000 13.76 7.41 46.89 4.70
3864 8027 5.263462 TTTTAACCGAAAAAGGCTTTCGCC 61.263 41.667 13.76 0.00 46.89 5.54
3873 8036 3.509659 GCTTTCGCCCCGCTTTAT 58.490 55.556 0.00 0.00 0.00 1.40
3874 8037 2.697819 GCTTTCGCCCCGCTTTATA 58.302 52.632 0.00 0.00 0.00 0.98
3875 8038 1.235724 GCTTTCGCCCCGCTTTATAT 58.764 50.000 0.00 0.00 0.00 0.86
3876 8039 2.419667 GCTTTCGCCCCGCTTTATATA 58.580 47.619 0.00 0.00 0.00 0.86
3877 8040 3.007635 GCTTTCGCCCCGCTTTATATAT 58.992 45.455 0.00 0.00 0.00 0.86
3878 8041 4.186159 GCTTTCGCCCCGCTTTATATATA 58.814 43.478 0.00 0.00 0.00 0.86
3879 8042 4.632688 GCTTTCGCCCCGCTTTATATATAA 59.367 41.667 0.81 0.81 0.00 0.98
3880 8043 5.122711 GCTTTCGCCCCGCTTTATATATAAA 59.877 40.000 15.47 15.47 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 120 8.133024 TGTAATTAACAGGCCAAAGATCAATT 57.867 30.769 5.01 3.87 33.01 2.32
120 121 7.716799 TGTAATTAACAGGCCAAAGATCAAT 57.283 32.000 5.01 0.00 33.01 2.57
138 139 9.308000 TGTGGACCAAGAATAAATTCTGTAATT 57.692 29.630 5.99 0.00 45.83 1.40
139 140 8.739972 GTGTGGACCAAGAATAAATTCTGTAAT 58.260 33.333 5.99 0.00 45.83 1.89
140 141 7.721842 TGTGTGGACCAAGAATAAATTCTGTAA 59.278 33.333 5.99 0.00 45.83 2.41
141 142 7.227873 TGTGTGGACCAAGAATAAATTCTGTA 58.772 34.615 5.99 0.00 45.83 2.74
142 143 6.068010 TGTGTGGACCAAGAATAAATTCTGT 58.932 36.000 5.99 1.30 45.83 3.41
143 144 6.573664 TGTGTGGACCAAGAATAAATTCTG 57.426 37.500 5.99 0.00 45.83 3.02
145 146 6.863126 CAGTTGTGTGGACCAAGAATAAATTC 59.137 38.462 0.00 0.00 37.06 2.17
146 147 6.549364 TCAGTTGTGTGGACCAAGAATAAATT 59.451 34.615 0.00 0.00 0.00 1.82
147 148 6.016276 GTCAGTTGTGTGGACCAAGAATAAAT 60.016 38.462 0.00 0.00 0.00 1.40
148 149 5.298276 GTCAGTTGTGTGGACCAAGAATAAA 59.702 40.000 0.00 0.00 0.00 1.40
149 150 4.819630 GTCAGTTGTGTGGACCAAGAATAA 59.180 41.667 0.00 0.00 0.00 1.40
150 151 4.385825 GTCAGTTGTGTGGACCAAGAATA 58.614 43.478 0.00 0.00 0.00 1.75
151 152 3.214328 GTCAGTTGTGTGGACCAAGAAT 58.786 45.455 0.00 0.00 0.00 2.40
152 153 2.639065 GTCAGTTGTGTGGACCAAGAA 58.361 47.619 0.00 0.00 0.00 2.52
153 154 1.472552 CGTCAGTTGTGTGGACCAAGA 60.473 52.381 0.00 0.00 0.00 3.02
154 155 0.937304 CGTCAGTTGTGTGGACCAAG 59.063 55.000 0.00 0.00 0.00 3.61
155 156 1.092921 GCGTCAGTTGTGTGGACCAA 61.093 55.000 0.00 0.00 0.00 3.67
156 157 1.522806 GCGTCAGTTGTGTGGACCA 60.523 57.895 0.00 0.00 0.00 4.02
157 158 1.522806 TGCGTCAGTTGTGTGGACC 60.523 57.895 0.00 0.00 0.00 4.46
158 159 1.087202 TGTGCGTCAGTTGTGTGGAC 61.087 55.000 0.00 0.00 0.00 4.02
159 160 1.087202 GTGTGCGTCAGTTGTGTGGA 61.087 55.000 0.00 0.00 0.00 4.02
160 161 1.351707 GTGTGCGTCAGTTGTGTGG 59.648 57.895 0.00 0.00 0.00 4.17
161 162 1.012343 CGTGTGCGTCAGTTGTGTG 60.012 57.895 0.00 0.00 0.00 3.82
162 163 0.529773 ATCGTGTGCGTCAGTTGTGT 60.530 50.000 0.00 0.00 39.49 3.72
163 164 0.161658 GATCGTGTGCGTCAGTTGTG 59.838 55.000 0.00 0.00 39.49 3.33
164 165 0.249280 TGATCGTGTGCGTCAGTTGT 60.249 50.000 0.00 0.00 39.49 3.32
165 166 1.059692 GATGATCGTGTGCGTCAGTTG 59.940 52.381 0.00 0.00 39.49 3.16
166 167 1.067565 AGATGATCGTGTGCGTCAGTT 60.068 47.619 0.00 0.00 39.49 3.16
167 168 0.528017 AGATGATCGTGTGCGTCAGT 59.472 50.000 0.00 0.00 39.49 3.41
168 169 1.633561 AAGATGATCGTGTGCGTCAG 58.366 50.000 0.00 0.00 39.49 3.51
169 170 2.078849 AAAGATGATCGTGTGCGTCA 57.921 45.000 0.00 0.00 39.49 4.35
170 171 2.222819 GGAAAAGATGATCGTGTGCGTC 60.223 50.000 0.00 0.00 39.49 5.19
171 172 1.732259 GGAAAAGATGATCGTGTGCGT 59.268 47.619 0.00 0.00 39.49 5.24
172 173 2.002586 AGGAAAAGATGATCGTGTGCG 58.997 47.619 0.00 0.00 39.92 5.34
173 174 2.029728 CGAGGAAAAGATGATCGTGTGC 59.970 50.000 0.00 0.00 0.00 4.57
174 175 3.511699 TCGAGGAAAAGATGATCGTGTG 58.488 45.455 0.00 0.00 35.05 3.82
175 176 3.868757 TCGAGGAAAAGATGATCGTGT 57.131 42.857 0.00 0.00 35.05 4.49
176 177 4.363138 TCATCGAGGAAAAGATGATCGTG 58.637 43.478 0.00 0.00 45.61 4.35
177 178 4.655762 TCATCGAGGAAAAGATGATCGT 57.344 40.909 0.00 0.00 45.61 3.73
182 183 6.206243 AGCCATATTTCATCGAGGAAAAGATG 59.794 38.462 26.72 27.03 43.99 2.90
183 184 6.206243 CAGCCATATTTCATCGAGGAAAAGAT 59.794 38.462 26.72 19.68 39.94 2.40
184 185 5.528690 CAGCCATATTTCATCGAGGAAAAGA 59.471 40.000 26.72 18.45 39.94 2.52
185 186 5.755813 CAGCCATATTTCATCGAGGAAAAG 58.244 41.667 26.72 18.84 39.94 2.27
186 187 4.036734 GCAGCCATATTTCATCGAGGAAAA 59.963 41.667 26.72 16.79 39.94 2.29
187 188 3.565482 GCAGCCATATTTCATCGAGGAAA 59.435 43.478 25.43 25.43 40.72 3.13
188 189 3.141398 GCAGCCATATTTCATCGAGGAA 58.859 45.455 8.70 8.70 0.00 3.36
189 190 2.104622 TGCAGCCATATTTCATCGAGGA 59.895 45.455 0.00 0.00 0.00 3.71
190 191 2.497138 TGCAGCCATATTTCATCGAGG 58.503 47.619 0.00 0.00 0.00 4.63
191 192 3.669824 GCATGCAGCCATATTTCATCGAG 60.670 47.826 14.21 0.00 37.23 4.04
192 193 2.227149 GCATGCAGCCATATTTCATCGA 59.773 45.455 14.21 0.00 37.23 3.59
193 194 2.030628 TGCATGCAGCCATATTTCATCG 60.031 45.455 18.46 0.00 44.83 3.84
194 195 3.314553 GTGCATGCAGCCATATTTCATC 58.685 45.455 23.41 0.00 44.83 2.92
195 196 2.287970 CGTGCATGCAGCCATATTTCAT 60.288 45.455 23.41 0.00 44.83 2.57
196 197 1.065851 CGTGCATGCAGCCATATTTCA 59.934 47.619 23.41 0.00 44.83 2.69
197 198 1.066002 ACGTGCATGCAGCCATATTTC 59.934 47.619 23.41 4.73 44.83 2.17
198 199 1.066002 GACGTGCATGCAGCCATATTT 59.934 47.619 23.41 0.00 44.83 1.40
199 200 0.664761 GACGTGCATGCAGCCATATT 59.335 50.000 23.41 0.00 44.83 1.28
200 201 0.464193 TGACGTGCATGCAGCCATAT 60.464 50.000 23.41 2.57 44.83 1.78
201 202 0.464193 ATGACGTGCATGCAGCCATA 60.464 50.000 23.41 7.35 44.83 2.74
202 203 1.317431 AATGACGTGCATGCAGCCAT 61.317 50.000 23.41 20.16 44.83 4.40
203 204 0.676151 TAATGACGTGCATGCAGCCA 60.676 50.000 23.41 18.80 44.83 4.75
204 205 0.664761 ATAATGACGTGCATGCAGCC 59.335 50.000 23.41 13.50 44.83 4.85
205 206 2.480224 AATAATGACGTGCATGCAGC 57.520 45.000 23.41 14.94 45.96 5.25
206 207 4.497966 CAGAAAATAATGACGTGCATGCAG 59.502 41.667 23.41 17.33 37.28 4.41
207 208 4.413969 CAGAAAATAATGACGTGCATGCA 58.586 39.130 18.46 18.46 37.28 3.96
208 209 3.241322 GCAGAAAATAATGACGTGCATGC 59.759 43.478 11.82 11.82 37.28 4.06
209 210 4.413969 TGCAGAAAATAATGACGTGCATG 58.586 39.130 3.82 3.82 37.28 4.06
210 211 4.700268 TGCAGAAAATAATGACGTGCAT 57.300 36.364 0.00 0.00 39.43 3.96
211 212 4.023279 AGTTGCAGAAAATAATGACGTGCA 60.023 37.500 0.00 0.00 37.66 4.57
212 213 4.475944 AGTTGCAGAAAATAATGACGTGC 58.524 39.130 0.00 0.00 0.00 5.34
213 214 6.991485 AAAGTTGCAGAAAATAATGACGTG 57.009 33.333 0.00 0.00 0.00 4.49
214 215 6.640907 GGAAAAGTTGCAGAAAATAATGACGT 59.359 34.615 0.00 0.00 0.00 4.34
215 216 6.640499 TGGAAAAGTTGCAGAAAATAATGACG 59.360 34.615 0.00 0.00 0.00 4.35
216 217 7.945033 TGGAAAAGTTGCAGAAAATAATGAC 57.055 32.000 0.00 0.00 0.00 3.06
217 218 7.118101 GCATGGAAAAGTTGCAGAAAATAATGA 59.882 33.333 0.00 0.00 33.40 2.57
218 219 7.238571 GCATGGAAAAGTTGCAGAAAATAATG 58.761 34.615 0.00 0.00 33.40 1.90
219 220 6.372381 GGCATGGAAAAGTTGCAGAAAATAAT 59.628 34.615 0.00 0.00 33.40 1.28
220 221 5.700373 GGCATGGAAAAGTTGCAGAAAATAA 59.300 36.000 0.00 0.00 33.40 1.40
221 222 5.011943 AGGCATGGAAAAGTTGCAGAAAATA 59.988 36.000 0.00 0.00 33.40 1.40
222 223 4.067192 GGCATGGAAAAGTTGCAGAAAAT 58.933 39.130 0.00 0.00 33.40 1.82
223 224 3.134442 AGGCATGGAAAAGTTGCAGAAAA 59.866 39.130 0.00 0.00 33.40 2.29
224 225 2.699846 AGGCATGGAAAAGTTGCAGAAA 59.300 40.909 0.00 0.00 33.40 2.52
225 226 2.318908 AGGCATGGAAAAGTTGCAGAA 58.681 42.857 0.00 0.00 33.40 3.02
226 227 1.999648 AGGCATGGAAAAGTTGCAGA 58.000 45.000 0.00 0.00 33.40 4.26
227 228 2.825861 AAGGCATGGAAAAGTTGCAG 57.174 45.000 0.00 0.00 33.40 4.41
228 229 4.888326 ATTAAGGCATGGAAAAGTTGCA 57.112 36.364 0.00 0.00 34.77 4.08
229 230 5.482006 AGAATTAAGGCATGGAAAAGTTGC 58.518 37.500 0.00 0.00 0.00 4.17
230 231 7.967890 AAAGAATTAAGGCATGGAAAAGTTG 57.032 32.000 0.00 0.00 0.00 3.16
231 232 9.489084 GTTAAAGAATTAAGGCATGGAAAAGTT 57.511 29.630 0.00 0.00 31.81 2.66
232 233 8.870116 AGTTAAAGAATTAAGGCATGGAAAAGT 58.130 29.630 0.00 0.00 31.81 2.66
236 237 9.920946 AGATAGTTAAAGAATTAAGGCATGGAA 57.079 29.630 0.00 0.00 31.81 3.53
237 238 9.561069 GAGATAGTTAAAGAATTAAGGCATGGA 57.439 33.333 0.00 0.00 31.81 3.41
238 239 9.342308 TGAGATAGTTAAAGAATTAAGGCATGG 57.658 33.333 0.00 0.00 31.81 3.66
261 262 9.106070 TCAATTGATGATGTTACTCAATCTGAG 57.894 33.333 3.38 2.09 40.82 3.35
279 280 3.827876 TGAGCACCACAACATCAATTGAT 59.172 39.130 15.36 15.36 33.57 2.57
280 281 3.220940 TGAGCACCACAACATCAATTGA 58.779 40.909 11.26 11.26 33.57 2.57
281 282 3.646611 TGAGCACCACAACATCAATTG 57.353 42.857 0.00 0.00 35.59 2.32
282 283 5.653330 TGATATGAGCACCACAACATCAATT 59.347 36.000 0.00 0.00 0.00 2.32
283 284 5.195185 TGATATGAGCACCACAACATCAAT 58.805 37.500 0.00 0.00 0.00 2.57
284 285 4.587891 TGATATGAGCACCACAACATCAA 58.412 39.130 0.00 0.00 0.00 2.57
285 286 4.219264 TGATATGAGCACCACAACATCA 57.781 40.909 0.00 0.00 0.00 3.07
286 287 5.297527 TGATTGATATGAGCACCACAACATC 59.702 40.000 0.00 0.00 0.00 3.06
287 288 5.195185 TGATTGATATGAGCACCACAACAT 58.805 37.500 0.00 0.00 0.00 2.71
288 289 4.587891 TGATTGATATGAGCACCACAACA 58.412 39.130 0.00 0.00 0.00 3.33
289 290 4.036027 CCTGATTGATATGAGCACCACAAC 59.964 45.833 0.00 0.00 0.00 3.32
290 291 4.201657 CCTGATTGATATGAGCACCACAA 58.798 43.478 0.00 0.00 0.00 3.33
291 292 3.812262 CCTGATTGATATGAGCACCACA 58.188 45.455 0.00 0.00 0.00 4.17
292 293 2.551459 GCCTGATTGATATGAGCACCAC 59.449 50.000 0.00 0.00 0.00 4.16
293 294 2.487805 GGCCTGATTGATATGAGCACCA 60.488 50.000 0.00 0.00 0.00 4.17
294 295 2.157738 GGCCTGATTGATATGAGCACC 58.842 52.381 0.00 0.00 0.00 5.01
295 296 3.137446 AGGCCTGATTGATATGAGCAC 57.863 47.619 3.11 0.00 0.00 4.40
296 297 5.013391 TCAATAGGCCTGATTGATATGAGCA 59.987 40.000 23.01 8.18 38.17 4.26
297 298 5.494724 TCAATAGGCCTGATTGATATGAGC 58.505 41.667 23.01 0.00 38.17 4.26
298 299 5.585445 GCTCAATAGGCCTGATTGATATGAG 59.415 44.000 25.18 20.37 41.31 2.90
299 300 5.013391 TGCTCAATAGGCCTGATTGATATGA 59.987 40.000 25.18 14.08 41.31 2.15
300 301 5.250982 TGCTCAATAGGCCTGATTGATATG 58.749 41.667 25.18 18.79 41.31 1.78
301 302 5.509832 TGCTCAATAGGCCTGATTGATAT 57.490 39.130 25.18 7.01 41.31 1.63
302 303 4.980339 TGCTCAATAGGCCTGATTGATA 57.020 40.909 25.18 18.57 41.31 2.15
303 304 3.870538 TGCTCAATAGGCCTGATTGAT 57.129 42.857 25.18 8.26 41.31 2.57
304 305 3.870538 ATGCTCAATAGGCCTGATTGA 57.129 42.857 24.22 24.22 40.23 2.57
305 306 5.123502 GTCATATGCTCAATAGGCCTGATTG 59.876 44.000 17.99 19.58 35.92 2.67
306 307 5.221986 TGTCATATGCTCAATAGGCCTGATT 60.222 40.000 17.99 8.54 0.00 2.57
310 311 4.923516 ATGTCATATGCTCAATAGGCCT 57.076 40.909 11.78 11.78 0.00 5.19
324 325 6.982724 TGCATCACAAACAACAAAATGTCATA 59.017 30.769 0.00 0.00 31.81 2.15
392 393 1.312815 GGGCTCCTCCATTTGAATCG 58.687 55.000 0.00 0.00 36.21 3.34
413 414 2.613506 CCAAACGTTCGCCCCTGTC 61.614 63.158 0.00 0.00 0.00 3.51
431 432 1.674817 CGGTCATCCAACCCTGTGTAC 60.675 57.143 0.00 0.00 35.79 2.90
482 483 7.201453 CGAACGGTGTACATCAAAACATACATA 60.201 37.037 6.97 0.00 30.67 2.29
548 549 7.390718 ACACTTTAGACAACTATTTGGATGGAC 59.609 37.037 0.00 0.00 37.00 4.02
602 603 0.911769 TTGGATCGATGCCTTGGAGT 59.088 50.000 14.82 0.00 0.00 3.85
613 614 1.259142 TACGGGGCTGTTTGGATCGA 61.259 55.000 0.00 0.00 0.00 3.59
614 615 0.810031 CTACGGGGCTGTTTGGATCG 60.810 60.000 0.00 0.00 0.00 3.69
777 781 9.213799 ACGTTGCCAAAAATACATAAATTTCAT 57.786 25.926 0.00 0.00 0.00 2.57
980 3236 4.474846 CCAATTCGCCAACCGCCG 62.475 66.667 0.00 0.00 36.73 6.46
981 3237 4.794439 GCCAATTCGCCAACCGCC 62.794 66.667 0.00 0.00 36.73 6.13
984 3240 1.226660 CATCGCCAATTCGCCAACC 60.227 57.895 0.00 0.00 0.00 3.77
985 3241 1.226660 CCATCGCCAATTCGCCAAC 60.227 57.895 0.00 0.00 0.00 3.77
986 3242 3.062500 GCCATCGCCAATTCGCCAA 62.063 57.895 0.00 0.00 0.00 4.52
987 3243 3.517140 GCCATCGCCAATTCGCCA 61.517 61.111 0.00 0.00 0.00 5.69
1289 3555 4.903649 TCATTGAGGATGAAGATAGAGGCA 59.096 41.667 0.00 0.00 41.73 4.75
1335 3603 5.555966 TCAGAAATGTACACATAACAGCCA 58.444 37.500 0.00 0.00 35.10 4.75
1337 3605 7.076842 ACATCAGAAATGTACACATAACAGC 57.923 36.000 0.00 0.00 35.10 4.40
1350 3622 6.368791 CCCATACATACCGTACATCAGAAATG 59.631 42.308 0.00 0.00 31.27 2.32
1360 3634 2.889045 TCAGCTCCCATACATACCGTAC 59.111 50.000 0.00 0.00 31.27 3.67
1361 3635 3.232720 TCAGCTCCCATACATACCGTA 57.767 47.619 0.00 0.00 0.00 4.02
1364 3638 4.929808 CGTAATTCAGCTCCCATACATACC 59.070 45.833 0.00 0.00 0.00 2.73
1505 3809 8.295288 GTCAATTGATACATCTGAATCCAATCC 58.705 37.037 12.12 0.00 0.00 3.01
1558 3980 8.023128 CACCATCTGTACAAAGTTAATTTCTGG 58.977 37.037 0.00 0.00 0.00 3.86
1573 3995 8.200792 AGAAAACTATCATCTCACCATCTGTAC 58.799 37.037 0.00 0.00 0.00 2.90
1657 4083 5.886960 ATCAGTGATTCCTGTTGTTAAGC 57.113 39.130 0.00 0.00 34.02 3.09
1682 4108 8.153411 CGAACCAAGTTAATTTCAATTTTAGCG 58.847 33.333 0.00 0.00 0.00 4.26
1782 4213 3.377172 GTGTTCTTCCCATTTACATCCCG 59.623 47.826 0.00 0.00 0.00 5.14
1788 4219 5.508994 CCCAGTTTGTGTTCTTCCCATTTAC 60.509 44.000 0.00 0.00 0.00 2.01
1893 4342 4.273318 AGCCCAAATTCATCTTGGTAGAC 58.727 43.478 1.23 0.00 41.60 2.59
1950 4399 3.238597 GGAAGCCTACATCTGAGGAGAT 58.761 50.000 0.00 0.00 39.75 2.75
2006 4829 7.770433 AGATAAATGCACTTGTAGTCAATGCTA 59.230 33.333 0.00 0.00 37.20 3.49
2138 5123 7.771183 TCCATTTAGATGCCAATTAACAGTTC 58.229 34.615 0.00 0.00 31.67 3.01
3000 7065 7.848051 CGATTAACTTAGTTCACTGCATCATTC 59.152 37.037 0.00 0.00 0.00 2.67
3246 7346 4.216257 AGTGACAAATGTTCATCTTTCCGG 59.784 41.667 0.00 0.00 0.00 5.14
3283 7386 8.983702 ACAAACCACGGTATAAATATGGTATT 57.016 30.769 0.00 0.00 42.90 1.89
3312 7416 3.079578 ACAGAAGTGACCATGAGCAATG 58.920 45.455 0.00 0.00 35.89 2.82
3506 7645 8.121305 ACAGGCAACATGTATCTAAAATGAAA 57.879 30.769 0.00 0.00 41.41 2.69
3548 7689 5.700402 AAAGATCCTATGTACCAGCAAGT 57.300 39.130 0.00 0.00 0.00 3.16
3551 7692 6.553953 TTGTAAAGATCCTATGTACCAGCA 57.446 37.500 0.00 0.00 0.00 4.41
3827 7990 7.922505 TTCGGTTAAAATCATGAGTTGTTTG 57.077 32.000 9.49 0.00 0.00 2.93
3829 7992 8.934507 TTTTTCGGTTAAAATCATGAGTTGTT 57.065 26.923 9.49 0.00 36.94 2.83
3830 7993 7.651704 CCTTTTTCGGTTAAAATCATGAGTTGT 59.348 33.333 9.49 2.86 36.94 3.32
3831 7994 7.359181 GCCTTTTTCGGTTAAAATCATGAGTTG 60.359 37.037 9.49 0.00 36.94 3.16
3832 7995 6.645003 GCCTTTTTCGGTTAAAATCATGAGTT 59.355 34.615 1.80 1.80 36.94 3.01
3833 7996 6.015434 AGCCTTTTTCGGTTAAAATCATGAGT 60.015 34.615 0.09 0.00 36.94 3.41
3834 7997 6.389906 AGCCTTTTTCGGTTAAAATCATGAG 58.610 36.000 0.09 0.00 36.94 2.90
3835 7998 6.339587 AGCCTTTTTCGGTTAAAATCATGA 57.660 33.333 0.00 0.00 36.94 3.07
3836 7999 7.420184 AAAGCCTTTTTCGGTTAAAATCATG 57.580 32.000 0.00 0.00 36.94 3.07
3837 8000 6.364976 CGAAAGCCTTTTTCGGTTAAAATCAT 59.635 34.615 12.72 0.00 45.17 2.45
3838 8001 5.688176 CGAAAGCCTTTTTCGGTTAAAATCA 59.312 36.000 12.72 0.00 45.17 2.57
3839 8002 6.136007 CGAAAGCCTTTTTCGGTTAAAATC 57.864 37.500 12.72 0.00 45.17 2.17
3857 8020 6.730960 TTTATATATAAAGCGGGGCGAAAG 57.269 37.500 12.90 0.00 0.00 2.62
3858 8021 6.730960 CTTTATATATAAAGCGGGGCGAAA 57.269 37.500 25.10 1.66 41.69 3.46
3876 8039 9.768662 AAAATCATGAGTTGTTCTTTGCTTTAT 57.231 25.926 9.49 0.00 0.00 1.40
3877 8040 9.598517 AAAAATCATGAGTTGTTCTTTGCTTTA 57.401 25.926 9.49 0.00 0.00 1.85
3878 8041 8.496707 AAAAATCATGAGTTGTTCTTTGCTTT 57.503 26.923 9.49 0.00 0.00 3.51


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.